A Unified Generative Framework for Scalable Chemical Reaction Network Exploration

Abstract

Chemical reaction networks (CRNs) are crucial for understanding reaction mechanisms and guiding chemical synthesis, yet the computational exploration remains limited by the combinatorial growth of chemical space, the reliability of reaction path screening, and the cost of evaluating thermodynamic and kinetic properties. Here, we present ByteCRN, an end-to-end framework for computational CRN exploration that combines chemically informed reaction enumeration with generative transition state modeling. A key component of our framework is a generative rectified flow architecture for both transition state generation and reaction validation, where it maps reactant-product pairs to candidate transition state structures and verifies connectivity by mapping back to reactants and products. This unified generative strategy replaces the most expensive steps of conventional computational workflows, namely iterative transition state search and intrinsic reaction coordinate validation, within a complete CRN construction pipeline. ByteCRN delivers a 10--100-fold acceleration over traditional workflows while maintaining high predictive fidelity for individual reactions. At the network scale, it effectively prunes $\sim$70-90% of the enumerated reactions, streamlining the exploration of complex reaction space. Its utility is illustrated through the discovery of novel pathways involving cyanoacetaldehyde and the successful modeling of the challenging $γ$-ketohydroperoxide network, demonstrating a practical, scalable approach to autonomous chemical exploration.